1. The CACCC box is a DNA sequence that functions as a positive transcriptional regulatory element in the promoters of several genes. The rat malic enzyme (ME) gene promoter contains two CACCC boxes at a site containing a tandem repeat of the sequence CTCGCCACCC (malic promoter element 2 or MPE2, -74/-48) which functions as a cis-regulatory element. A sequence similar to a half-site of MPE2 is found in the human immunodeficiency virus long terminal repeat (HIV, LTR, -67/-42) and the human c-fos promoter also contains a sequence identified as a retinoblastoma control element (RCE, -100/-70) which is similar to MPE2. We have now obtained two proteins binding to this site: 1. By screening a rat liver cDNA expression library with the MEP2 binding site and 2. using HeMEP2 DNA as an affinity matrix in purifying a protein from a rat liver nuclear extracts. Both proteins bind specifically to this site. However they also interact specifically with the malic enzyme thyroid hormone response element. Thus the same or similar nuclear proteins bind to two separate transcriptional cis-regulatory elements in the ME gene promoter one of which also binds the T3 receptor. These liver nuclear proteins may play important roles in the ME gene transcriptional response to thyroid hormone. Further characterization of these proteins and DNA motifs to which they bind is being investigated. 2. The alpha and beta receptors are highly related to each other, bind the same ligand, and to the same TREs, but they give quantitatively different responses when activated by hormone suggesting that they do not have redundant functions. The T3 receptor alpha variant protein exerts distinct effects on transactivating functions of these receptors by a mechanism that is still unclear.